Project Iceberg
by SilverLunaMoon
Summary: When NCIS gets a new case, they never thought it would be this complicated. A dead marine whife, a disappeared marine and a kidnapped son, soon evolves into something that might threaten even the national security. And what about the 8 year old kid? Story is dead!
1. Prologue

**A/N: **

Yeah, I know I should upload the next chapter of Mission Hogwarts, it's on it's way. But I had this plot bunny that just wouldn't let go!

So here it is:D A Naruto/NCIS crossover. Some info first, this is set somewhere in season 2 of NCIS and is a modern AU for the Naruto characters. That means no ninjas. The prologue is rather short, but I promise that the first chapter will be longer :D

I don't own NCIS nor do I own Naruto.

_Edit: Had forgotten to put in time  
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**Project Iceberg**

**Prologue**

**Day 7 - 15:46  
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"And when he finally admitted Dre was right, he actually pouted. Can you imagine that? It was hilarious!"

Three boys were walking down a sidewalk. The smallest one, looking roughly eight years old with black hair and dark eyes, walked backwards with a backpack on his shoulders while looking at his two companions.

"Really?" one of the two walking the right way said with a small smile on his face. He had the same black eyes as the smallest child, but had longer hair which was tied at the base of his neck. He looked thirteen or fourteen years old. "Walk properly Sasuke" he scolded.

The youngest, Sasuke, pouted briefly before turning around and walking straight again.

The last one, the eldest, had shorter, curlier hair and a wide grin plastered on his face. He was the tallest one, and by the looks of it, seemed to be sixteen or seventeen. He was the one who had first spoken.

"Why can't I be with you two?" Sasuke whined.

"Don't you want to play with Naruto today?" the long haired boy asked, slightly amused.

"Yeah… but I want to be with you too"

"Heh, you sure have a whiney brother, don't you Itachi?" the tallest one said while grinning.

"I'm not! You're mean Shisui!" Sasuke said angrily, turning around again.

"I'm just being truthful" Shisui said, still grinning while Itachi chuckled.

"Hmpf"

They all turned left and into a smaller road with houses on both sides. Itachi walked over the road and towards a white coloured house, similar to many other houses in the street.

Sasuke stayed on the same side of the road and walked towards a yellow house and rang the bell.

After a few seconds, the door opened and in it stood a yellow haired man.

"Hello Sasuke, come to see Naruto?" the man said.

Sasuke nodded before wriggling past the adult and into the house.

"Yo! Mr. Namikaze" Shisui yelled from the road, far higher than necessary.

"Hello Shisui. And you know you can call me Minato." Minato said with a grin. Even after having known each other for over four years, Shisui still called Minato for Mr. Namikaze, though mostly just to tease him.

"You and Itachi going somewhere?" he asked.

By now Shisui had walked over to Minato so he didn't need to yell. "Nah, we're only going over to my place. I've just gotten a new game and managed to get Itachi to come and try two-players with me." He turned around to look at the house Itachi had entered. "He's just dumping his schoolbag first" Minato nodded.

They hear some rustling behind Minato and turned to see Sasuke and an eight year old Minato-look-alike putting on shoes. "We're going out to play in the yard!" the look-alike said.

"Sure thing Naruto" Minato said, making room for them to go out.

Sasuke stopped on his way out, looking towards his own home.

"What is it?" Naruto asked.

"The car is there," he said.

"So?"

Sasuke turned to look at Naruto. "Mom and dad aren't supposed to be home now," he looked back "it's just that."

"Shisui, where are you going?" Minato asked as Shisui started to walk away from them.

"Just getting Itachi, he's been away for a while." the teen answered.

Shisui made his way over the road and waked in the front door.

"Itachi?" he half yelled. "Aren't we supposed to go?"

No answer.

'Strange…' Shisui thought as he made his way through the house.

Both the kitchen and Itachi's room were empty and Shisui started to get a bad feeling. His eyes wandered the hall and finally rested on the door to the living room.

What was that smell?

As he got closer he started to smell something, almost like iron.

He opened the door and stood frozen. There in front of him lay Mikoto Uchiha, Itachi and Sasuke's mother, in a pool of blood and with unseeing eyes.

Before he could utter a sound, he heard a sound to his right and turned just as he saw something big coming straight towards his head.

And then… darkness.

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**Day 7 - 15:50**

Itachi walked in the door to his home.

He had noticed the car was home and expected someone to be home, but couldn't hear anything as he entered.

"Mom?" He said, waiting for a response. "Dad?"

The teen walked into his room and dropped off his schoolbag, before taking his phone out of one of his pockets.

No messages or calls.

He shrugged it off and put the phone back in the pocket. They had probably just used the bus for once; they sometimes did that, and not told them. Itachi still decided to check the rest of the house. He had a bad feeling and couldn't just ignore it.

He knew something was wrong when he entered his father's home office**_._**the teen immediately saw what was wrong. Several folders were open and empty and papers were spread all over the floor. He looked towards the desk and noticed the computer was gone as well.

Itachi quickly exited the room and was half way running towards the outdoor when he heard a sound of something hitting the floor in the living room.

Against his better judgement he walked towards the door and opened it fully.

Itachi's eyes travelled the room for a brief second before resting on the unmoving form on the floor.

"M-mom?" he half whispered, before running towards her.

Or he would have, if he hadn't been ambushed.

He suddenly felt someone grip him from behind and press something soft over his mouth and nose and he could smell a sweet scent from it.

'Chloroform' Itachi realised with dread.

It had barely been over his mouth for a second and he was loosing his consciousness as well as seeing his vision blacken.

The last Itachi saw was the lifeless eyes of his mother.

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**Day 7 - 15:57**

"Hmm?" Minato looked away from the two playing kids in his garden as he heard the sound of a car.

The blond man could see a black SUV pull up outside Itachi and Sasuke's house. The windows were blackened so he couldn't see any driver, nor could he see any passengers.

But he could see a black dressed man run out of the house with an unconscious body over his shoulder.

"HEY!" he yelled as he ran towards the car.

"ITACHI!" He could hear Sasuke scream behind him, but his eyes were focused on the car.

The man came opened the door to the back seat and jumped in with the unconscious Itachi before slamming it shut again.

Minato had to jump away from the road to not get run over as the car drove out of the alley and out of sight.

Minato looked over to his house and saw his wife had come out and was restraining a screaming and crying Sasuke with Naruto who was trying to calm him down.

He did the only thing he could, he called the police.

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**A/N:**

So? You like?

Please R&R and see ya soon^^


	2. Ch 1 New Case

**A/N:  
><strong>Yup, I'm actually updating. Isn't that amasing? Anyway, a few important things before you sart reading the chapter.

**O**ne, you should go back to the prologe and check out the time and day I've put in, it's going to be important :P I managed for some reason to forget it ^^' **S**econd, warnings, totally forgot that... um, character deaths (a bit too late for that one, right?), blood, violence, dunno if it's going to me as much as/graphic enough to an M rating, but just watch out for that.  
><strong>T<strong>hird, this is NOT a romance! I might include some parings or at least hints of it, and they can be both homosexual and hetrosexual couples/parings. But doubt anything more than hints. you people are able to survive that.

Think that was all...

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**Chapter 1 - The Case**

**Day 7 – 16:25 – NCIS HQ**

Kate groaned slightly as she took another look at the paperwork at her desk. It was bigger than normal and she had a feeling it was due to Tony's rather small one.

"Have you seen the new movie yet Kate?" McGee spoke up from his desk while looking at some of his own work.

"What movie?" she asked, looking up at him.

"Harry Potter"

"No, haven't seen it yet," Kate answered, looking back at the papers in her hand.

"Which one?" Tony Dinozzo spoke up from behind his desk.

"What?" Kate said, slightly confused.

"Well, aren't there like, a dozen or something?"

"No, there's eight, the last one just came out," McGee answered Tony. "Aren't you supposed to know everything about every movie?"

"I know everything about every _good_ movie McGeek"

"The Harry Potter series is one of the most popular movies in the world, Tony" Kate retorted before McGee could.

"Only fantasy geeks think so. Like you guys"

McGee rolled his eyes.

"And anyways, when a movie gets too many sequels, it always gets worse"

"What exactly gets worse?" a voice said from behind Tony.

"Hi boss!" Tony said, leaning fast over the paperwork. "Um, the paperwork, boss. We have been working all day."

"You don't have much left, so when you finish, help Kate out with hers" Gibbs commanded before sitting down behind his own desk with a cup of coffee.

Tony scowled while Kate smiled sweetly at him.

They all sat behind their desks, engrossed in their own work until the phone at Gibb's desk rang.

"Yeah?" Gibbs answered after he picked up the phone. He listened to the voice at the other end for a few seconds before hanging up.

"Get ready" was all he said and stood up.

Instantly, Kate, Tony and Timonthy rose as well.

"Another case?" Tony asked.

"No, I just want some coffee," he slapped Tony behind the head. "Of course a new case"

"What happened?" Kate asked while getting her gun and badge and started to follow Gibbs towards the elevator.

"A marine wife has been kidnapped and the eldest son has been kidnapped" Gibbs informed them quickly.

Kate nodded. Gibbs always took a case more seriously, not that he ever took a case unseriously, when a kid was involved.

Gibbs took his phone and called Ducky. They were going to need him on the scene. After he closed the cell, he, Tony and Kate waited for McGee to get his backpack and enter the elevator before taking it down and towards the parking lot.

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**Day 7 – 16:52 – Outside of the Uchiha residence**

Gibbs walked out of the car with confidence and walked up to the police that had already arrived. Kate could also see an ambulance at the side of the road with a teen sitting in the opening, holding an icepack to his head and having a blanket around him.

She looked at the kid for a while until Gibbs waved her over.

"Where's Ducky?" Gibbs asked her.

"My guesses are on Palmer taking a wrong turn again" Tony answered.

As he said that, another NCIS car rolled over and in on the scene and the former Secret service agent saw Ducky and Palmer climbing out of it.

"You really shouldn't make this a habit Mr. Palmer" Ducky commented. "You know, this really reminds me of the time-"

"Ducky!" Gibbs called.

"Oh sorry" Ducky apologized as he came up to the team.

Gibbs stopped to talk to the police officer that was already on the scene before turning back to his own team.

"Kate, you go and talk to the witnesses" he nodded towards the ambulance closest to them and the teen who sat there. "His name is Shisui Taekeda. Apparently he was knocked out by the kidnappers. He is friends with the kid whom was kidnapped, Itachi Uchiha. You should also talk to the neighbours. Rest of you, with me" he motioned for them to follow him inside the house.

Kate walked over to the ambulance and said kid looked up as she approached.

"Hello there Shisui. I'm Caitlin Todd, NCIS, but you can call me Kate" she showed him the badge. "I need to ask you a few questions about the incident"

Shisui nodded as he shifted his icepack on his head.

"Can you tell me what happened?"

"He… he was just going to drop off his backpack" Shisui said. "We were going out and-" He stopped himself when he saw Kate's expression.

"That came out wrong" he said before looking away from Kate and to the crime scene instead.

"We were going over to my place and while he dropped of his stuff, I waited outside. Sasuke was playing with their neighbour and I talked to Minato" He stopped and looked over the street and towards another house.

"That's Minato," he said, pointing at a blonde man who stood and talked to a police man. "And that's Naruto, his son" he motioned to a blonde kid that sat just outside of the house with a black haired child.

"And Sasuke is the one with black hair?" Kate asked.

"Yes. Itachi's brother" Shisui informed her. "Anyway, I went after Itachi when he didn't come back. I noticed something was wrong when no one answered me. When I came into the living room… oh my god" Kate could hear his voice shaking. "Mikoto was just lying there… I talked to her this morning!"

Kate, not sure what to do, sat down besides him on the ambulance, and started to rub his back a little, waiting for him to continue.

"I heard something to my right, and when I turned, all I saw was something blunt smashing into my head. Woke up with a doctor beside me twenty minutes ago and Itachi… he was _gone_"

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**Day 7 – 16:59– Uchiha Residence, crime scene**

When Gibbs' team came into the room, Ducky immediately went over to the body of a woman lying on the floor.

"Oh my," the ME mumbled. "Palmer, over here" he said as he motioned for his assistant.

Gibbs motioned for the others to look around the room as he walked up to Ducky. "Well Ducky?"

"Jethro, I haven't even started," the doctor began before stopping himself sighing, "Her throat is cut, but I won't be able to say if that it the cause of death yet or not"

Gibbs nodded before looking around.

They were in the living room and it didn't seem like there had been much of a struggle. Not by first glance anyway.

What a mess. And no one still had been able to contact Fugaku Uchiha, the marine who lived here yet either.

"Boss!" Tony called and Gibbs turned. The Special Agent pointed towards something white on the floor and the former marine soldier could see it was cotton.

"Bag it" he told Dinozzo before turning to McGee who had just come through the door.

"I checked the other rooms. It seems like they wanted something from Fugaku Uchiha. His office is completely raided"

"Where is he?" Gibbs asked McGee.

"No one has seen him apparently. I tried calling where he worked, but they said he had called and said he was sick"

"What did he work with then?" Gibbs asked.

"Um…" Tim started. "Don't know, boss. I checked some of the paper files and they didn't say…" he trailed of as he saw Gibbs's expression. "I'll gather the files that's left in the room" he finished before going back out of the room

Gibbs watched his newest member walk out of the room before he turned to the doctor.

"Ducky?"

"I would put the time of death around 3PM" Ducky said, looking at Gibbs. "The poor woman seems to have sustained several bruises as well"

"She was beat up?"

"She put up a fight at least. I would need to get her home before being able to tell you any more"

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**Day 7 – 18:14 – Outside of the Uchiha residence**

The team met up again outside of the house.

Gibbs nodded. "We're going back"

"Um…" Kate started, making the others look at her.

"What about the kid?" McGee asked.

"He's going to stay with the neighbours for the moment. The boy doesn't have any other relatives and they all seemed rather close. I gave Mr. Namikaze our number in case something happened." Kate answered, having talked to the blond neighbour.

Gibbs accepted this explanation with a nod before turning and starting to walk towards their car.

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**Day 7 - 19:26 – NCIS HQ**

"What do we have?" Gibbs asked in a commanding voice to his team.

They were all currently back in their office, trying to work on the new case instead of thinking about their beds at home. Tony pulled up three pictures on their plasma screen, having one of them bigger than the others, before turning to look at the rest of his colleagues.

"Mikoto Uchiha," Tony started. "Age 39, married to Fugaku Uchiha and housewife. Nothing really special about her, yet she was murdered in her house"

Dinozzo clicked on the remote in his hand and the second picture was zoomed in on.

"Fugaku Uchiha, age 40 and no one currently knows where he is. He was last seen yesterday at work at the Pentagon" He turned from the screen to look at the rest of them. "Worked in Pentagon. Apparently, he worked on something alone, I talked to his secretary and she said she didn't know what he worked on"

Tony changed to the last picture.

"Itachi Uchiha, age 13. He's in 9th grade even though he's supposed to be in eighth"

"Why?" Kate asked, looking at the picture. The kid didn't seem like anyone special.

"Well, he's got top grades in school; and apparently, his father wanted him further up, but it was denied because the teachers believed it to be best that he was with people at his own age. Though the teachers did admit he was smart enough to go have gone up another year"

"Do we have anything that can help us?" said the impatient leader of the team. Had they nothing to work on?

"Abby is analysing the evidence we found and Ducky is working on the autopsy as we speak" answered McGee.

"And you?"

"Um… I'll try to find out what the kidnappers wanted from his computer" he said fast before hurrying to his desk, not risking the wrath of his boss.

Said boss turned to Kate and Tony.

"I'll try to find out where Mr. Uchiha was last seen" Kate explained, leaving Tony alone in front of Gibbs"

"I'm going to find someone who might now what he worked with" Tony said. "You know, with McGee looking through files and computer…stuff, I'll find someone who might actually have an idea to what he did"

Gibbs stared at him for a few seconds "Well, get started" he said before turning away and walking over to his own desk, seemingly in his own world.

What a mess.

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><strong>AN:**

Okay, I would love som constructive critisism on this (that means tell me what's wrong and not just say it's wrong ^^'). I have lacing skills in anything to do with America, and feel it hard to write the NCIS characters so I would love to hear what you thought.  
>Also, feel free to come with suggestions for the story, not everything in it is set in stone.<p>

The author loves reviews, they're like digital cookies :3


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